[R] How to see how a function is written
Sergey Goriatchev
sergeyg at gmail.com
Tue Jun 15 15:10:18 CEST 2010
> showMethods("apply")
Function: apply (package base)
X="ANY"
X="missing"
(inherited from: X="ANY")
X="timeSeries"
On Tue, Jun 15, 2010 at 15:10, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
> On Tue, 2010-06-15 at 14:56 +0200, Sergey Goriatchev wrote:
>> Maybe I have to much stuff loaded in the workspace, Gavin, you are right:
>
> OK, so now do
>
> showMethods("apply")
>
> And R should list out the available methods. See which package
> (re)defines apply.
>
> But it is likely going to be simpler to start a clean session and look
> at the code in there. If you need the S4 method/generic code then you'll
> have to find out which package is redefining apply and look in the
> sources for that package.
>
> HTH
>
> G
>
>> > sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=German_Switzerland.1252
>> LC_CTYPE=German_Switzerland.1252
>> LC_MONETARY=German_Switzerland.1252
>> [4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] PerformanceAnalytics_1.0.0 quantmod_0.3-13 TTR_0.20-1
>> Defaults_1.1-1 xts_0.7-0
>> [6] fPortfolio_2100.78 Rglpk_0.3-5 slam_0.1-9
>> fAssets_2100.78 fCopulae_2110.78
>> [11] sn_0.4-14 mnormt_1.3-3
>> fBasics_2110.79 timeSeries_2110.87 timeDate_2110.87
>> [16] robustbase_0.5-0-1 quadprog_1.4-12 MASS_7.3-5
>> fEcofin_290.76 foreach_1.3.0
>> [21] codetools_0.2-2 iterators_1.0.3 zoo_1.6-3
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.10.1 lattice_0.18-3 tools_2.10.1
>>
>>
>> On Tue, Jun 15, 2010 at 14:56, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
>> > On Tue, 2010-06-15 at 14:38 +0200, Sergey Goriatchev wrote:
>> >> Erik, I see the following when I type "apply" at the prompt:
>> >>
>> >> > apply
>> >> standardGeneric for "apply" defined from package "base"
>> >
>> > Looks like you have something loaded in your workspace (or have created
>> > something) that has altered the usual definition of apply(). Most likely
>> > is a package has made the base apply() function an S4 method.
>> >
>> > Send the output of sessionInfo() to the list so we can help if you
>> > interest is in the S4 method version of apply() (myself I'm not too
>> > familiar with S4 methods just yet).
>> >
>> > If you start R in a clean session, you should see the normal definition
>> > of apply
>> >
>> > R --vanilla
>> > apply
>> >
>> > On Windows you may need to add that option to the shortcut you use to
>> > start R.
>> >
>> > You could also try
>> >
>> > base:::apply
>> >
>> > to see the version in the base R namespace (at least I think that should
>> > work).
>> >
>> >>
>> >> function (X, MARGIN, FUN, ...)
>> >> standardGeneric("apply")
>> >> <environment: 0x03cad7d0>
>> >> Methods may be defined for arguments: X, MARGIN, FUN
>> >> Use showMethods("apply") for currently available ones.
>> >>
>> >> Also, whether I type "mean" at the prompt, or I type "edit(mean)", I
>> >> do not see the underlying code for function "mean". How would I be
>> >> able to see it?
>> >
>> > The info I sent in my previous email should help you with the mean
>> > function --- as long as that hasn't been overwritten by anything.
>> >
>> >> methods(mean)
>> > [1] mean.data.frame mean.Date mean.default mean.difftime
>> > [5] mean.POSIXct mean.POSIXlt
>> >> getS3method("mean", "default")
>> > function (x, trim = 0, na.rm = FALSE, ...)
>> > {
>> > if (!is.numeric(x) && !is.complex(x) && !is.logical(x)) {
>> > warning("argument is not numeric or logical: returning NA")
>> > return(NA_real_)
>> > }
>> > if (na.rm)
>> > x <- x[!is.na(x)]
>> > if (!is.numeric(trim) || length(trim) != 1L)
>> > stop("'trim' must be numeric of length one")
>> > n <- length(x)
>> > if (trim > 0 && n) {
>> > if (is.complex(x))
>> > stop("trimmed means are not defined for complex data")
>> > if (any(is.na(x)))
>> > return(NA_real_)
>> > if (trim >= 0.5)
>> > return(stats::median(x, na.rm = FALSE))
>> > lo <- floor(n * trim) + 1
>> > hi <- n + 1 - lo
>> > x <- sort.int(x, partial = unique(c(lo, hi)))[lo:hi]
>> > }
>> > .Internal(mean(x))
>> > }
>> > <environment: namespace:base>
>> >
>> > Although here, none of the mean methods are hidden so you could just
>> > type their names directly.
>> >
>> > The meaning of the .Internal( ) bit is that this calls internal C
>> > code. Uwe Ligges article discusses what to do at this point.
>> >
>> > HTH
>> >
>> > G
>> >
>> >>
>> >> ---
>> >> My machine:
>> >> platform i386-pc-mingw32
>> >> arch i386
>> >> os mingw32
>> >> system i386, mingw32
>> >> status
>> >> major 2
>> >> minor 10.1
>> >> year 2009
>> >> month 12
>> >> day 14
>> >> svn rev 50720
>> >> language R
>> >> version.string R version 2.10.1 (2009-12-14)
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Tue, Jun 15, 2010 at 14:26, Erik Iverson <eriki at ccbr.umn.edu> wrote:
>> >> > Sergey Goriatchev wrote:
>> >> >>
>> >> >> Hello,
>> >> >>
>> >> >> If I want to see how, say, apply function is written, how would I be
>> >> >> able to do that?
>> >> >> Just typing "apply" at the prompt does not work.
>> >> >>
>> >> >
>> >> > Well, it is supposed to work, and it works for me. So you need to tell us
>> >> > what "does not work" means, and all the info the posting guide requests, OS,
>> >> > versions, etc.
>> >> >
>> >>
>> >>
>> >>
>> >
>> > --
>> > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>> > Dr. Gavin Simpson [t] +44 (0)20 7679 0522
>> > ECRC, UCL Geography, [f] +44 (0)20 7679 0565
>> > Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
>> > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
>> > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
>> > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>> >
>> >
>>
>>
>>
>
> --
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> ECRC, UCL Geography, [f] +44 (0)20 7679 0565
> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
>
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